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- PDB-6ash: Crystal structure of human Cathepsin K with a non-active site inh... -

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Basic information

Entry
Database: PDB / ID: 6ash
TitleCrystal structure of human Cathepsin K with a non-active site inhibitor at 1.42 Angstrom resolution
ComponentsCathepsin K
KeywordsHYDROLASE/ HYDROLASE Inhibitor / cathepsin K / exosite / inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex / HYDROLASE / HYDROLASE- HYDROLASE Inhibitor complex
Function / homology
Function and homology information


cathepsin K / mononuclear cell differentiation / intramembranous ossification / negative regulation of cartilage development / cellular response to zinc ion starvation / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / thyroid hormone generation / endolysosome lumen / Trafficking and processing of endosomal TLR / proteoglycan binding ...cathepsin K / mononuclear cell differentiation / intramembranous ossification / negative regulation of cartilage development / cellular response to zinc ion starvation / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / thyroid hormone generation / endolysosome lumen / Trafficking and processing of endosomal TLR / proteoglycan binding / Activation of Matrix Metalloproteinases / cysteine-type endopeptidase activator activity involved in apoptotic process / mitophagy / fibronectin binding / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / bone resorption / cysteine-type peptidase activity / cellular response to transforming growth factor beta stimulus / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / lysosomal lumen / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / response to insulin / response to organic cyclic compound / cellular response to tumor necrosis factor / response to ethanol / lysosome / immune response / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / serine-type endopeptidase activity / intracellular membrane-bounded organelle / proteolysis / extracellular space / extracellular region / nucleoplasm
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
2-{[(carbamoylsulfanyl)acetyl]amino}benzoic acid / Cathepsin K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.423 Å
AuthorsLaw, S. / Aguda, A. / Nguyen, N. / Brayer, G. / Bromme, D.
Funding support Canada, 4items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-89974 Canada
Canadian Institutes of Health Research (CIHR)MOP-125866 Canada
Canadian Institutes of Health Research (CIHR)MOP-125866 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-326803-13 Canada
CitationJournal: To Be Published
Title: Crystal structure of human Cathepsin K with a non-active site inhibitor at 1.42 Angstrom resolution.
Authors: Law, S. / Brayer, G. / Bromme, D.
History
DepositionAug 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Structure summary
Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cathepsin K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2704
Polymers23,5071
Non-polymers7633
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.480, 60.400, 44.150
Angle α, β, γ (deg.)90.00, 95.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cathepsin K / / Cathepsin O / Cathepsin O2 / Cathepsin X


Mass: 23507.480 Da / Num. of mol.: 1 / Fragment: UNP residues 115-329 / Mutation: S49A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSK, CTSO, CTSO2 / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: P43235, cathepsin K
#2: Chemical ChemComp-1XF / 2-{[(carbamoylsulfanyl)acetyl]amino}benzoic acid


Mass: 254.262 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H10N2O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 8% polyethylene glycol (PEG) 4000, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.42→39.32 Å / Num. obs: 37046 / % possible obs: 95.5 % / Redundancy: 5.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Net I/σ(I): 24.2
Reflection shellResolution: 1.42→1.5 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.071 / Mean I/σ(I) obs: 14.9 / Num. unique obs: 5467 / CC1/2: 0.993 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
iMOSFLM7.2.1data reduction
SCALA3.3.22data scaling
PHASER1.8.1_1168phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X6H

4x6h


Resolution: 1.423→39.32 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 13.26
RfactorNum. reflection% reflection
Rfree0.1463 1822 4.92 %
Rwork0.1158 --
obs0.1173 37042 95.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.423→39.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1648 0 51 283 1982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141737
X-RAY DIFFRACTIONf_angle_d1.3762337
X-RAY DIFFRACTIONf_dihedral_angle_d16.558631
X-RAY DIFFRACTIONf_chiral_restr0.104231
X-RAY DIFFRACTIONf_plane_restr0.007310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.423-1.46150.16561310.0932778X-RAY DIFFRACTION98
1.4615-1.50450.16741430.09342692X-RAY DIFFRACTION96
1.5045-1.55310.14111420.08712672X-RAY DIFFRACTION95
1.5531-1.60860.13961250.08932567X-RAY DIFFRACTION91
1.6086-1.6730.15871520.08882782X-RAY DIFFRACTION98
1.673-1.74920.141470.0952716X-RAY DIFFRACTION97
1.7492-1.84140.13651370.09862710X-RAY DIFFRACTION94
1.8414-1.95670.13781230.09892623X-RAY DIFFRACTION93
1.9567-2.10780.1441430.10742784X-RAY DIFFRACTION98
2.1078-2.31990.1341420.11182728X-RAY DIFFRACTION96
2.3199-2.65550.15181570.12582660X-RAY DIFFRACTION95
2.6555-3.34540.15171470.13222753X-RAY DIFFRACTION96
3.3454-39.33740.14641330.1482755X-RAY DIFFRACTION95

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